WO2017042381A1

WO2017042381A1 - Means and methods for diagnosing familial mediterranean fever

Info

Publication number: WO2017042381A1
Application number: PCT/EP2016/071418
Authority: WO
Inventors: Mohamed Lamkanfi; Hanne Van Gorp; Pedro SAAVEDRA
Original assignee: Vib Vzw; Universiteit Gent
Priority date: 2015-09-11
Filing date: 2016-09-12
Publication date: 2017-03-16

Abstract

The present invention belongs to the field of autoinflammatory diseases, particularly to the diagnosis of autoinflammatory diseases, more particularly to the specific diagnosis and/or prognosis of familial Mediterranean fever (FMF). Accordingly the present invention provides methods and kits for the diagnostic use of FMF.

Description

Means and methods for diagnosing familial Mediterranean fever

Field of the invention

Introduction to the invention

Familial Mediterranean Fever (FMF) is the most common inherited monogenic autoinflammatory disease (AID) worldwide, and has an autosomal recessive inheritance (1 ). The gene mutated in these patients is MEFV, which encodes the inflammasome adaptor pyrin (2, 3). FMF is particularly common in the Middle East and the Mediterranean basin, including Jewish, Turkish, Armenian, Arab and Italian populations. In these regions, the prevalence of FMF is between 1 in 500 and 1 in 1000, and MEFV mutations are very common, with the carrier rate reaching 1 :5 to 1 :3 in certain ethnic groups (4). The prevalence of distinct variants in these populations suggests positive selection of these FMF-associated variants as the evolutionary mechanism. The disease has spread over the world with migrations of these populations over the past centuries (5). Recently, pyrin was shown to control inflammasome signaling, and based on this insight, FMF-associated variants in MEFV are currently thought to represent gain-of-function mutations, similar to cryopyrin-associated period fever mutations in NLRP3. However, the autosomal recessive inheritance of FMF is more aligned with a hitherto uncharacterized loss-of- function consequent to the disease-associated mutations. In the present invention we have identified for the first time such loss-of-function role for FMF-associated variants in regulation of non-inflammasome-dependent cytokine secretion, findings that have led to the development of a functional diagnostic screen that segregates FMF patients from patients suffering from other AID and healthy individuals. FMF usually has a childhood onset, and is characterized by recurrent attacks of fever associated with serositis. Its main long-term complication is amyloid A (AA) amyloidosis, a severe manifestation with poor prognosis. Colchicine remains the therapeutic choice to prevent both FMF attacks and complications. However, before committing to daily, lifelong treatment, it is crucial to establish an accurate diagnosis (5, 6). The diagnosis of FMF is primarily made on the basis of clinical symptoms, and is further supported by review of ethnic origin, family history and genetic information. Until recently, FMF was diagnosed in pediatric patients using clinical criteria that have been developed for adults. Delay in the appearance of the complete clinical picture in very young children, the presence of atypical signs, the absence of suggestive family history and uncertainty of the family provenance may cause additional diagnostic difficulties in this age group. Clinical diagnosis of FMF is also complicated l by similarities in the clinical picture with other (recently identified and some still uncharacterized) AID syndromes, and therefore confirmation is looked for via genetic diagnosis. At first, it was believed that genetic testing would enable physicians to completely resolve the diagnostic difficulties associated with FMF. However, interpretation of FMF genetic testing has proved challenging. To date, over 280 MEFV sequence variants have been reported, with many variants being highly prevalent in populations, and several rare variants having uncertain disease association. The diagnosis of FMF is straightforward in a patient with a suggestive phenotype and known mutations in both MEFV alleles. Also, most individuals with one mutation in MEFV are asymptomatic carriers of the disease. However, classical FMF may also occur in carriers of only a single MEFV mutation, while on the other hand carriers of two mutations may exhibit no overt signs of the disease (5-7). These issues can be largely overcome by functionally screening patients based on novel insight in the molecular functions and biological roles of pyrin. In the absence of such specific tests for FMF, in the present invention we have developed a functional assay that allows segregation of patients likely suffering from FMF on the one hand from healthy controls and patients suffering from other AID syndromes with overlapping clinical phenotypes on the other hand.

Description of Figures

Figure 1 : C. difficile activates an inflammasome via TcdA B in human PBMC.

Human Peripheral Blood Mononuclear Cells (PBMC) were prepared from 3 healthy donors. Cells were either pretreated with YVAD (50 μΜ) or left untreated prior to infection with C. difficile (MOI 0.1 ) for 21 hours (A, B). To assess the contribution of TcdA and TcdB, cells were infected with C. difficile (MOI 0.1 ), either wild-type or toxinA B-deficient, for 21 hours (C-F). Supernatant was collected to determine IL-1 beta (A, C), IL-18 (B, D), IL-6 (E) and TNF-alfa (F) cytokine levels.

Figure 2: C. difficile TcdA and TcdB activate an inflammasome in human PBMC. Human Peripheral Blood Mononuclear Cells (PBMC) were prepared from 3 healthy donors. Cells were either pretreated with YVAD (50 μΜ) or left untreated prior to stimulation with C. difficile TcdA (1 μg ml) or TcdB (1 μg ml) for 5 hours. Supernatant was collected to determine IL-1 beta (A, C) and IL-18 (B, D) cytokine levels.

Figure 3: Colchicine inhibits C. difficile TcdA-induced inflammasome signaling, while colchicine combined with MCC950 are required to fully block C. difficile TcdB-induced inflammasome signaling.

Human Peripheral Blood Mononuclear Cells (PBMC) were prepared from 3 healthy donors. Cells were either pretreated with colchicine (1 μΜ), MCC950 (10 μΜ) or a combination of both, or left untreated prior to stimulation with C. difficile TcdA (1 μg ml) or TcdB (1 μg ml) for 5 hours. Supernatant was collected to determine IL-1 beta (A, C), IL-18 (B, D), IL-6 (E) and TNF-alfa (F) cytokine levels.

Figure 4: In Familial Mediterranean Fever (FMF), C. d/7f/^'c//e-induced inflammasome signaling is enhanced, while non-inflammasome signaling is hampered. Genomic DNA from a healthy donor and an FMF patient was sequenced to confirm 2 heterozygous mutations (M694V and R761 H) in the FMF patient (A). IL-18 (B), IL-6 (C) and TNF-alfa (D) cytokine levels and S100A8/A9 (E) protein levels were determined in serum from 4 healthy donors (squares) and 1 1 patients with autoinflammatory diseases (circles), including one FMF patient indicated with a triangle. PBMC were prepared from 3 healthy donors (filled bars, different colors grey-black for different individuals) and 1 FMF patient (horizontal black and white stripes). Cells were infected with C. difficile (MOI 0.1 ) for 21 hours (F-l) or stimulated with C. difficile TcdA (1 μg ml) or TcdB (1 μg ml) for 5 hours (J-Q). Supernatant was collected to determine IL-1 beta (F, J, N), IL-18 (G, K, O), IL-6 (H, L, P) and TNF-alfa (I, M, Q) cytokine levels.

Figure 5: Colchicine treatment prior to C. difficile TcdA stimulation results in a distinct inflammasome cytokine profile in FMF patients compared to healthy controls and non-FMF patients suffering from autoinflammation.

PBMC were prepared from 5 healthy donors (circles), and patients suffering from an autoinflammatory disorder, more precisely 4 CAPS (diamonds), 7 JIA (squares) and 9 FMF (triangles) patients. Cells were treated for 30min with colchicine (1 μΜ) prior to stimulation with C. difficile TcdA (1 μg ml) for 5 hours. Supernatant was collected to determine IL-1 beta (A) and IL-18 (B) cytokine levels.

Figure 6: Colchicine treatment prior to C. difficile TcdB stimulation results in a distinct non- inflammasome cytokine profile in FMF patients compared to healthy controls and a non-FMF patient suffering from autoinflammation. PBMC were prepared from 3 healthy donors (filled bars, different colors grey-black for different individuals), 1 FMF patient (horizontal black and white stripes) and 1 non-FMF patient (black and white squares) suffering from an autoinflammatory disorder (AID). Cells were treated for 30min with colchicine (1 μΜ) prior to stimulation with C. difficile TcdB (1 μg ml) for 5 hours. Supernatant was collected to determine IL-6 (A, C) and TNF-alfa (B, D) cytokine levels. Figure 7: different microtubule polymerization inhibitors can be used prior to the stimulation with C. difficile TcdA on PBMC. PBMC were prepared from healthy donors (circles) and FMF patients (triangles). Cells were treated for 30min with colchicine (1 μΜ), nocodazole (1 μΜ), ABT-751 (1 μΜ), CA4P (1 μΜ) and CYT997 (1 μΜ) prior to stimulation with C. difficile TcdA (1 Mg/ml) for 5 hours. Figure 8: Colchicine treatment prior to C. difficile TcdA stimulation results in distinct ASC speck formation in FMF patients compared to healthy controls and a non-FMF patients suffering from autoinflammation. PBMC were prepared from healthy donors (HC), FMF patients (FMF) and non-FMF patients suffering from an autoinflammatory disorder (AID), examplified by CAPS (rhombus) and JIA (square). Cells were treated for 30min with colchicine (1 μΜ) prior to stimulation with C. difficile TcdA (1 μg ml) for 5 hours. Next, cells were fixed and an immunofluorescence staining was performed visualizing cell nuclei with DAPI and ASC specks (arrows indicate specks in the figure). Images were acquired using a spinning-disk confocal microscope and the percentage of cells containing an ASC speck were quantified using 3D image analysis software Volocity. Statistical analysis was performed using a t-test.

Figure 9: PBMC were prepared from 4 healthy donors (circles), 4 FMF carriers (heterozygous; squares) and 4 FMF patients (homozygous or compound heterozygous; triangles). Cells were treated for 30min with colchicine (1 μΜ) prior to stimulation with C. difficile TcdA (1 μg ml) for 5 hours. Supernatant was collected to determine IL-1 beta (A), IL-18 (B), IL-6 (C) and TNF (D) cytokine levels.

Detailed description of the invention

As used herein, each of the following terms has the meaning associated with it in this section. The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element. "About" as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1 %, and still more preferably ±0.1 % from the specified value, as such variations are appropriate to perform the disclosed methods. The term "abnormal" when used in the context of organisms, tissues, cells or components thereof, refers to those organisms, tissues, cells or components thereof that differ in at least one observable or detectable characteristic (e.g., age, treatment, time of day, etc.) from those organisms, tissues, cells or components thereof that display the "normal" (expected) respective characteristic. Characteristics which are normal or expected for one cell or tissue type, might be abnormal for a different cell or tissue type. The drawings described are only schematic and are non-limiting. In the drawings, the size of some of the elements may be exaggerated and not drawn on scale for illustrative purposes. Where the term "comprising" is used in the present description and claims, it does not exclude other elements or steps. Furthermore, the terms first, second, third and the like in the description and in the claims, are used for distinguishing between similar elements and not necessarily for describing a sequential or chronological order. It is to be understood that the terms so used are interchangeable under appropriate circumstances and that the embodiments, of the invention described herein are capable of operation in other sequences than described or illustrated herein. Unless specifically defined herein, all terms used herein have the same meaning as they would to one skilled in the art of the present invention. Practitioners are particularly directed to Sambrook et al., Molecular Cloning: A Laboratory Manual, 4^th ed., Cold Spring Harbor Press, Plainsview, New York (2012); and Ausubel et al., current Protocols in Molecular Biology (Supplement 100), John Wiley & Sons, New York (2012), for definitions and terms of the art. The definitions provided herein should not be construed to have a scope less than understood by a person of ordinary skill in the art.

Autoinflammatory diseases are a group of disorders characterized by seemingly unprovoked inflammation in the absence of infective causes, autoantibodies or auto-reactive T-lymphocytes, that derive from defects in innate immunity. Most are genetic in origin. Familial Mediterranean fever (FMF) is the most prevalent inherited monogenic autoinflammatory disease, mainly affecting ethnic groups living along the eastern Mediterranean coast: Sephardic Jews, Armenians, Turks, and Arabs. FMF is not rare in other Mediterranean basin ethnicities, such as Druze, Greeks and Italians. The disease is characterized by irregular, short inflammatory episodes of serositis, accompanied by fever. Amyloidosis, the most significant complication of FMF, is the major cause of mortality and may be prevented by for example colchicine prophylactic treatment. As autoinflammatory diseases have overlapping symptoms, diagnostic criteria are essential to assure accurate diagnosis and appropriate medical follow-up and treatment of FMF. 'Compound heterozygosity' or 'compound heterozygous' in medical genetics is the condition of having two heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state. An organism is a compound heterozygote when it has two recessive alleles for the same gene, but with those two alleles being different from each other (for example, both alleles might be mutated but at different locations).

The present invention satisfies this need and provides diagnostic methods for the accurate detection of FMF.

Accordingly in a first embodiment the invention provides an in vitro diagnostic method to identify a patient suffering from familial Mediterranean fever (FMF) comprising the following steps: a. incubating a pyrin-activating microbial agent with a patient sample comprising peripheral blood mononuclear cells (PBMC),

b. quantifying the level of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 optionally in combination with the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in said sample, c. comparing the levels of cytokines in step b) with at least one sample derived from an individual not suffering from FMF and d. identifying a patient suffering from FMF if the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced with respect to the value from an individual not suffering from FMF and/or if the level of at least one inflammasome independent cytokine is at least 4-fold reduced with respect to the value from an individual not suffering from FMF.

In yet another embodiment the invention provides an in vitro diagnostic method to identify a patient suffering from familial Mediterranean fever (FMF) comprising the following steps:

a. incubating a pyrin-activating microbial agent with a patient sample comprising peripheral blood mononuclear cells (PBMC),

b. quantifying the level of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 in combination with the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in said sample,

c. comparing the levels of cytokines in step b) with at least one sample derived from an individual not suffering from FMF and

d. identifying a patient suffering from FMF if the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced with respect to the value from an individual not suffering from FMF and if the level of at least one inflammasome independent cytokine is at least 4-fold reduced with respect to the value from an individual not suffering from FMF.

b. quantifying the level of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 and the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in said sample,

d. identifying a patient suffering from FMF if the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced with respect to the value from an individual not suffering from FMF and if the level of at least one inflammasome independent cytokine is at least 4-fold reduced with respect to the value from an individual not suffering from FMF. In yet another embodiment the invention provides an in vitro diagnostic method to distinguish a patient suffering from familial Mediterranean fever (FMF) from heterozygous FMF carriers and from individuals not suffering from FMF comprising the following steps:

a. pretreating a patient sample comprising peripheral blood mononuclear cells (PBMC) with a microtubule polymerization inhibitor,

b. incubating the pretreated sample with a pyrin-activating microbial agent,

c. quantifying the level of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 and the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in said sample,

d. comparing the levels of cytokines in step b) with at least one sample derived from an individual not suffering from FMF and

e. identifying a patient suffering from FMF if the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced with respect to the value from an individual not suffering from FMF and if the level of at least one inflammasome independent cytokine is at least 4-fold reduced with respect to the value from an individual not suffering from FMF; identifying a heterozygous FMF carrier if the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced with respect to the value from an individual not suffering from FMF and if the level of at least one inflammasome independent cytokine is similar to the value from an individual not suffering from FMF.

In the context of the present invention a patient suffering from familial Mediterranean fever (FMF) is also called an FMF patient. An FMF patient can be homozygous or compound heterozygous. An FMF patients suffers from (or has) the hallmarks of FMF. An FMF carrier is a person having a heterozygous mutation (also called here a heterozygous FMF carrier) and an FMF carrier does not suffer from the disease hallmarks (or symptoms) of FMF. Also "an individual not suffering from FMF" can be a healthy individual or can also be an individual suffering from an autoimmune disease which is different from FMF. An individual not suffering from FMF is not a heterozygous FMF carrier.

The wording "an inflammasome independent cytokine" can be used interchangeably with the wording "an NF-kappaB dependent cytokine".

Hence the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced, is at least 5-fold enhanced, at least 10-fold enhanced, at least 50-fold enhanced, at least 100- fold enhanced, at least 500-fold enhanced or at least 1000-fold enhanced. The term "enhanced" is equivalent to "increased" or "higher than". Hence the level of at least one inflammasome independent cytokine is at least 4-fold, at least 10-fold reduced, at least 50-fold reduced, at least 100-fold reduced, at least 500-fold reduced or at least 1000-fold reduced. The term "reduced" is equivalent to "lower than" or "less than".

A peripheral blood mononuclear cell (PBMC) is any blood cell having a round nucleus (as opposed to a lobed nucleus). A PBMC cell can be a lymphocyte, a monocyte, a dendritic cell or a macrophage. These blood cells are a critical component in the immune system to fight infection and adapt to intruders. These cells can for example be extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, and gradient centrifugation, which will separate the blood into a top layer of plasma, followed by a layer of PBMCs and a bottom fraction of polymorphonuclear cells (such as neutrophils and eosinophils) and erythrocytes. The polymorphonuclear cells can be further isolated by lysing the red blood cells. Basophils are sometimes found in both the denser and the PBMC fractions.

In yet another embodiment in the in vitro diagnostic method the peripheral blood mononuclear cells are pretreated with a microtubule polymerization inhibitor prior to incubation with a pyrin- activating microbial agent.

Microtubule polymerization inhibitors are well known in the art and comprise several compounds such as colchicine, nocodazole, ABT-751 , CA4P and CYT997. In the present invention it is shown in Figure 7 that different structural classes of microtubule polymerization inhibitors have a similar effect on peripheral blood mononuclear cells derived from FMF patients prior to the incubation with a pyrin-activating microbial agent with respect to the stimulation of the secretion of I L1 -beta and IL-18.

In a specific embodiment the in vitro diagnostic method the peripheral blood mononuclear cells are pretreated with colchicine prior to incubation with a pyrin-activating microbial agent.

a incubating a patient sample comprising peripheral blood mononuclear cells (PBMC) with colchicine, followed by incubating the sample with the Clostridium difficile TcdA toxin,

b quantifying the level of at least one inflammasome dependent cytokine such as IL- 1 beta or IL-18 in said sample,

c comparing the levels of cytokines in step b) with the levels of cytokines in at least one sample derived from an individual not suffering from FMF and

d identifying a patient suffering from FMF if the level of at least one inflammasome dependent cytokine is at least 50-, at least 100-, at least 500-, or at least 1000-fold enhanced with respect to the value from an individual not suffering from FMF with respect to the value from an individual not suffering from FMF.

a. incubating a patient sample comprising peripheral blood mononuclear cells (PBMC) with colchicine, followed by incubating the sample with the Clostridium difficile TcdB toxin,

b. quantifying the level of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in said sample,

c. comparing the levels of cytokines in step b) with the levels of cytokines in at least one sample derived from an individual not suffering from FMF and

d. identifying a patient suffering from FMF if the level of at least one inflammasome independent cytokine is at least 50-, at least 100-, at least 500- or at least 1000-fold lower with respect to the value from an individual not suffering from FMF. Pyrin-activating microbial agents comprise the use of Burkholderia cenocepacia bacteria, Clostridium difficile bacteria, toxins TcdA and TcdB derived from Clostridium difficile, Clostridium botulinum C3 toxin, Vibrio parahaemolyticus VopS toxin, Histophilus somni IbpA toxin and pertussis toxin.

In specific embodiments in the in vitro diagnostic methods of the invention the control sample value is a previously determined value from healthy individuals and/or from patients suffering from an autoinflammatory disease different from FMF.

In yet another embodiment the invention comprises a kit for diagnosing FMF comprising at least one pyrin-activating microbial agent and reagents for detecting at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 optionally in combination with a reagent for detecting at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL- 12 or TNF.

In yet another embodiment the invention comprises a kit for diagnosing FMF comprising at least one pyrin-activating microbial agent, colchicine and reagents for detecting at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 optionally in combination with a reagent for detecting at least one inflammasome independent cytokine such as for example IL- 4, IL-6, IL-12 or TNF.

In yet another embodiment the invention comprises a kit for diagnosing FMF comprising the Clostridium difficile toxin TcdA, colchicine and reagents for detecting at least one inflammasome dependent cytokine such as IL-1 beta or IL-18. In yet another embodiment the invention comprises a kit for diagnosing FMF comprising the Clostridium difficile toxin TcdB, colchicine and reagents for detecting at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF.

In yet another embodiment the invention provides a prognostic method for identifying an FMF patient responding to therapy comprising the following steps: a. quantifying the level of at least one inflammasome dependent cytokine such as IL- 1 beta or IL-18 optionally in combination with the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF in a PBMC sample derived from said patient,

b. comparing the levels of quantified cytokines in step a) with a PBMC patient sample obtained before starting the therapy and

c. attributing a response to therapy when the levels of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 are statistically lower than before the therapy and/or when the levels of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF are statistically higher than before the therapy.

The wording "statistically lower" means for example that the levels are at least 2-fold, at least 5- fold, at least 10-fold, at least 50-fold, at least 100-fold lower or even lower.

The wording "statistically higher" means for example that the levels are at least 2-fold, at least 5-fold, at least 10-fold, at least 50-fold, at least 100-fold higher or even higher.

In particular embodiments in the prognostic method the therapy comprises the use of colchicine, interferon-alpha, TNF-inhibitors or IL-1 antagonists.

Several therapeutic options are available for the treatment of FMF patients. Colchicine is usually the first option to prevent attacks of familial Mediterranean fever (FMF) and preventing the development of amyloidosis. Colchicine is administered daily in patients at risk of developing amyloidosis (e.g. North African Jewish people, Turkish people and Armenian people living in Armenia). Other Sephardic Jewish people and Arabic people are at lower risk but also probably require daily colchicine therapy. Ashkenazi Jewish people and Armenian people living in America seem to be at extremely low risk of amyloidosis and may need treatment only to prevent attacks. If attacks are rare and patients can determine when they are beginning, treatment with intermittent colchicine therapy at the onset of attacks may be sufficient. The regimen for acute attacks in patients not taking daily colchicine is 0.6 mg every hour for 4 doses, then 0.6 mg every 2 hours for 2 doses and then 0.6 mg every 12 hours for 4 doses. Colchicine should be started as soon as the patient recognizes that an attack is occurring. If the initial doses are effective, patients may be able to do without the later doses, but this varies from patient to patient. In patients whose conditions do not respond to colchicine, the use of interferon-alpha, the tumor necrosis factor-blocking drug etanercept, and the IL-1 receptor antagonist anakinra may be effective. Rilonacept, a once-weekly subcutaneous injection IL-1 decoy receptor, has been shown, in combination with continuation of colchicine, to reduce the number of attacks in patients who did not respond optimally. Interferon-alpha has been used in an intermittent fashion and as prophylaxis, with varying results.

Measuring and quantifying cytokines

Although some cytokines are produced at ng/ml concentrations in body fluids, most are expressed at pg/ml levels. This is the main reason that traditional methods of proteomics, such as 2D gel electrophoresis and mass spectrometry, are less preferred for cytokine detection. Immunoassays are capable of detecting most of these low-abundance proteins. There are several methods of detecting and analyzing cytokines in a sample: traditional ELISA assays, enzyme-linked immunosorbent spot (ELIspot) assays, antibody array assays and bead-based assays. It is up to the skilled person to choose the method to carry out the methods of the invention. Traditional ELISA assays are reliable, tried-and-true solutions that many researchers depend on. A successful ELISA system depends on having good antibodies and detection reagents for the assay. In the drawback category, ELISA assays are not fast, and they usually require larger sample volumes than the other assay types.

In addition to the use of protein-based identification assays for the detection of cytokines. It is also possible to quantify the expression of cytokines, particularly inflammasone-dependent cytokines, at the level of mRNA. Suitable methods are for example quantititative RT-PCR methods. In yet another embodiment the invention provides an in vitro diagnostic method to identify a patient suffering from familial Mediterranean fever (FMF) comprising the following steps:

a. incubating a patient sample comprising PBMC with a microtubule polymerization inhibitor, followed by incubating the sample with a pyrin-activating agent,

b. comparing the presence of ASC specks with the presence in at least one sample derived from an individual not suffering from FMF, and

c. wherein the presence of ASC specks identifies a patient suffering from FMF.

a. incubating a patient sample comprising PBMC with a microtubule polymerization inhibitor, followed by incubating the sample with a pyrin-activating agent, b. comparing the presence of ASC specks with the presence in at least one sample derived from an individual not suffering from FMF, and

c. wherein the presence of at least 5-times more ASC specks identifies a patient suffering from FMF.

c. wherein the presence of at least 10-times more ASC specks identifies a patient suffering from FMF. In yet another embodiment the invention provides an in vitro diagnostic method to identify a patient suffering from familial Mediterranean fever (FMF) comprising the following steps:

a. incubating a patient sample comprising PBMC with colchicine, followed by incubating the sample with TcdA,

c. wherein the presence of ASC specks identifies a patient suffering from FMF.

In yet another embodiment the invention provides a prognostic method for identifying an FMF patient responding to therapy comprising the following steps:

a. quantifying the presence of ASC specks in a PBMC sample derived from said patient, b. comparing the levels of quantified ASC specks in step a) with a PBMC patient sample obtained before starting the therapy and c. attributing a response to therapy when the levels of ASC specks are statistically lower than before the therapy.

In yet another embodiment the invention provides a kit for diagnosing FMF comprising a pyrin- activation microbial agent, a tubulin polymerization inhibitor and reagents for detecting ASC specks such as ASC specific antibodies.

The following examples are intended to promote a further understanding of the present invention. While the present invention is described herein with reference to illustrated embodiments, it should be understood that the invention is not limited hereto. Those having ordinary skill in the art and access to the teachings herein will recognize additional modifications and embodiments within the scope thereof. Therefore, the present invention is limited only by the claims attached herein.

Examples

1 . C. difficile induces inflammasome activation in human PBMC via TcdA B Infection of human PBMC with C. difficile results in inflammasome activation. This is supported by the observation that pretreatment of cells with the caspase-1 inhibitor Ac-YVAD-cmk abrogates IL-1 beta and IL-18 secretion (see Figure 1A, B). Furthermore, inflammasome activation is driven by toxins A and B because a non-toxigenic strain of C. difficile is unable to induce secretion of the inflammasome-dependent cytokines IL-1 beta and IL-18, while the non- inflammasome related cytokines IL-6 and TNF-alfa are secreted normally in the presence of the caspase-1 inhibitor (see Figure 1 C-F).

Next, the specific contribution of TcdA and TcdB in inflammasome activation was studied in more detail. Both toxins induce secretion of the caspase-1 -dependent cytokines IL-1 beta and IL-18, which is largely inhibited when cells are pretreated with the caspase-1 inhibitor Ac-YVAD-cmk (see Figure 2A-D).

2. TcdA signals through the pyrin inflammasome, while TcdB signals through the pyrin and NLRP3 inflammasomes

Colchicine is a natural compound mostly known for its ability to inhibit microtubule polymerization. It is highly effective in preventing fever attacks and delaying long-term amyloidosis in patients diagnosed with FMF, and is therefore used as the therapy of choice in FMF, although its mode of action is not known so far. Pretreatment of PBMC with colchicine prevents TcdA-induced inflammasome activation as indicated by the lack of IL-1 beta and IL-18 secretion (see Figure 3A, B), similar to our observations with the caspase-1 inhibitor Ac-YVAD- cmk pretreatment (see Figure 2A, B). These results suggest that colchicine inhibits pyrin inflammasome activation by TcdA.

Unlike with TcdA, colchicine treatment prior to TcdB stimulation resulted only in partial reduction of secreted IL-18 levels. Surprisingly, under these conditions we observed increased levels of IL-1 alfa as well as IL-6 and TNF-alfa in culture supernatants (see Figure 3C-F). Further reduction in secreted IL-18 levels was observed when cells were pretreated with colchicine in combination with the NLRP3-specific inhibitor MCC950 (see Figure 3D), indicating that TcdB activates the pyrin as well as the NLRP3 inflammasomes. This is further supported by the abrogated IL-1 beta response after TcdB stimulation of colchicine/MCC950 pretreated PBMC (see Figure 3C). Notably, the combination of MCC950 and colchicine pretreatment did not modulate the TcdB- induced secretion of the non-inflammasome-dependent cytokines IL-6 and TNF-alfa (see Figure 3E, F). This indicates that the NLRP3 inflammasome contributes to TcdB-induced secretion of IL-1 beta and IL-18, but not IL-6 and TNF-alfa.

3. C. difficile infection of human PBMC can be used as a functional screen to identify FMF patients based on elevated IL-1 beta and IL-18 levels in FMF patients compared to healthy controls

Familial Mediterranean Fever (FMF) is the most common autoinflammatory disorder (AID). It is a genetic disease caused by mutations in the MEFV (pyrin) gene. Serum samples from several patients suffering from AID were analyzed for cytokine and alarmin levels. A patient diagnosed with FMF that was genetically confirmed (see Figure 4A) had increased levels of IL-18 and S100A8/A9 in serum relative to healthy controls and a subset of AID patients of uncharacterized etiology. Unlike the increased IL-18 levels in the FMF patient, IL-6 and TNF-alfa levels in this patient were normal (see Figure 4B-E). Notably, ex vivo C. difficile infection of PBMC of the FMF patient resulted in enhanced inflammasome-dependent secretion of IL-1 beta and IL-18 compared to PBMC of healthy controls (see Figure 4F-I). Therefore, infection of human PBMC with C. difficile can be used as a functional screen to identify FMF patients.

4. C. difficile TcdA and TcdB stimulation of human PBMC can be used as a functional screen to identify FMF patients based on elevated IL-18 levels, reduced IL-6 and TNF-alfa levels or combinations thereof

Not only C. difficile infection results in a distinct cytokine profile in FMF patients, but also TcdA or TcdB stimulation can be used as a functional screen to identify FMF patients. Similar as observed with C. difficile infection, stimulation of PBMC with either toxin results in elevated IL- 18 levels in the FMF patient compared to cells from healthy controls (see Figure 4K-0). In contrast, IL-1 beta was not increased in FMF PBMC over healthy controls exposed to TcdA or TcdB (see Figure 4J-N). Importantly, FMF PBMC were hampered in secretion of non- inflammasome-dependent cytokines in response to TcdA or TcdB stimulation as demonstrated by the dampened IL-6 and TNF-alfa levels relative to those of healthy controls (see Figure 4L- M, P-Q).

5. Colchicine and TcdA stimulation of human PBMC can be used as a functional screen to identify FMF patients based on a distinct inflammasome-induced cytokine secretion profile in

FMF patients compared to healthy controls and non-FMF AID patients

As described above, colchicine pre-treatment blocks the TcdA-induced inflammasome response in healthy individuals (see Figure 3A-B). Interestingly, this is not the case in FMF patients, colchicine-pre-treated PBMC of which secrete significant levels of the inflammasome-dependent cytokines IL-1 beta and IL-18 after TcdA stimulation (see Figure 5A-B). Similar to healthy controls, colchicine pre-treatment potently inhibited TcdA-induced inflammasome responses in PBMC of non-FMF AID patients, more precisely patients suffering from CAPS and JIA, (see Figure 5A-B), further supporting the potential use of colchicine in combination with TcdA as a functional screen to specifically identify FMF patients over healthy controls and patients suffering from other AID.

6. Colchicine and TcdB stimulation of human PBMC can be used as a functional screen to identify FMF patients based on a distinct non-inflammasome cytokine secretion profile in FMF patients compared to healthy controls and non-FMF AID patients

As described above, colchicine treatment prior to TcdB stimulation results in secretion of elevated levels of non-inflammasome-related cytokines IL-6 and TNF-alfa from PBMC of healthy individuals (see Figure 3E-F). Interestingly, this does not hold in FMF patients, colchicine- pretreated PBMCs of which do not secrete significant levels of IL-6 and TNF-alfa in response to TcdB (see Figure 6A-D). This profile is specific for FMF because PBMC of an non-FMF AID patient responded similarly to cells from healthy individuals and secreted elevated levels of IL-6 and TNF-alfa after TcdB stimulation and colchicine pretreatment (see Figure 6C, D). These observations support defective secretion of non-inflammasome-dependent cytokines from PBMC treated with colchicine in combination with TcdB as a functional screen to specifically identify FMF patients between healthy individuals and other AID patients.

7. Colchicine and TcdA stimulation of human PBMC can be used as a functional screen to identify FMF patients based on distinct inflammasome-induced ASC speck formation in FMF patients compared to healthy controls and non-FMF AID patients

Activation of inflammasomes triggers the concomitant self-oligomerization of the bipartite PYD- CARD adaptor protein ASC into a single 'ASC speck' with prion-like properties (Cai X. et al. (2014) Cell, 156(6): 1207); Lu ei a/.(2014) Cell 156(6):1 193). These ASC specks can be detected by means of appropriate ASC-specific antibodies using well-established fluorescence microscopy imaging, FACS and biochemical enrichment methodologies. In this example (see Figure 8), we demonstrate that TcdA-induced ASC speck numbers were significantly reduced in colchicine-pre-treated PBMCs of FMF patients with at least one disease-associated FMF allele, but not in PBMCs of healthy controls expressing wildtype Pyrin. Similar to healthy controls, colchicine pre-treatment potently inhibited TcdA-induced ASC speck formation in PBMC of non- FMF AID patients, exemplified by CAPS (Cryopyrin-associated Autoinflammatory Syndromes) and JIA (Juvenile idiopathic arthritis) patients (see Figure 8), further supporting the potential use of ASC speck detection as a functional screen to specifically identify FMF patients over healthy controls and patients suffering from other AID.

8. Colchicine and TcdA stimulation of human PBMC can be used as a functional screen to discriminate healthy controls, FMF carriers (heterozygous), and FMF patients (homozygous or compound heterozygous) based on a distinct cytokine profile combining both inflammasome- and non-inflammasome-induced cytokines As described above, colchicine pre-treatment blocks the TcdA-induced inflammasome response in healthy individuals (see Figure 3A-B) and not in FMF patients (homozygous or compound heterozygous; see Figure 5A-B). Interestingly, FMF carriers (heterozygous) behave like FMF patients with respect to their inflammasome response after colchicine and TcdA treatment, more precisely colchicine is not able to block TcdA-induced inflammasome signaling in FMF carriers (see Figure 9A-B). As indicated above, FMF patients have an hampered non-inflammasome cytokine response upon TcdA and TcdB stimulation (see Figure 4L-M, P-Q). This still holds true even following colchicine pre-treatment (see Figure 9C-D). Interestingly, in the case of non- inflammasome cytokines, FMF carriers behave like healthy donors with normal responses following colchicine-TcdA treatment (see Figure 9C-D). Therefore, the combination of inflammasome- and non-inflammasome-induced cytokine responses following colchicine-TcdA treatment can be used as a functional screen to discriminate between healthy individuals, FMF carriers (heterozygous) and FMF patients (homozygous or compound heterozygous).

Materials and methods

1 . Human serum and PBMC

Peripheral venous blood specimens were collected from healthy individuals as well as from patients suffering from autoinflammatory syndromes (AID). Serum was obtained from blood collected in Vacutainer Serum tubes. Human peripheral blood mononuclear cells (PBMCs) on the other hand were isolated from blood collected in EDTA-coated Vacutainer tubes followed by Ficoll-Hypaque density gradient centrifugation. After isolation, PBMCs were used either fresh or stored in liquid nitrogen for later usage. Upon thawing, PBMCs were allowed to recover for 1 hour at 37°C in culture medium consisting of RPMI supplemented with 10% FBS. Following cell viability determination, cells were seeded at a density of 2.5 x 10⁵ per 96-well and maintained in a 5% C0₂ incubator at 37°C.

2. Sequencing

Genomic DNA was isolated from purified PBMCs and used as a template for subsequent variant detection. Exon 10 of MEFV was amplified using MEFV-specific primers extended with universal M13 sequences. The PCR product was sequenced in both directions using Sanger Sequencing.

3. Bacteria

Clostridium difficile strains VP110463 (toxigenic; A⁺B⁺) and VPI 1 1 186 (non-toxigenic; A^"B^") were purchased from ATCC. Glycerol stocks were cultured overnight at 37°C in anaerobic conditions in BHIS enriched medium (37 g/l brain heart infusion - Gibco; 5 g/l yeast extract - Gibco; 0.03% L-cysteine - Sigma; 0.1 % sodium taurocholate - Sigma).

4.Stimulations and infections

In some experiments, cells were pretreated with colchicine (1 μΜ; Sigma), MCC950 (10 μΜ) or ac-YVAD-cmk (50 μΜ; Enzo Life Sciences) for 30 minutes prior stimulation. C. difficile infection experiments were performed by infecting PBMCs (MOI 0.1 ) for 21 hours. Alternatively, cells were stimulated with TcdA or TcdB from C. difficile (1 μg ml; Enzo Life Sciences) for 5hours.

5.Cytokine analysis

IL-1 beta, IL-18, IL-6 and TNF-alfa cytokine levels were determined in cell culture supernatants and serum using a multiplex assay (Luminex; Bio-Rad). S100A8/A9 levels were determined in serum using an ELISA assay.

References

1 . Masters SL, Simon A, Aksentijevich I, Kastner DL. 2009. Horror autoinflammaticus: the molecular pathophysiology of autoinflammatory disease. Annual review of immunology 27:621 - 668. 2. Balow JE, Jr., Shelton DA, Orsborn A, Mangelsdorf M, Aksentijevich I, Blake T, Sood R, Gardner D, Liu R, Pras E, Levy EN, Centola M, Deng Z, Zaks N, Wood G, Chen X, Richards N, Shohat M, Livneh A, Pras M, Doggett NA, Collins FS, Liu PP, Rotter Jl, Kastner DL, et al. 1997. A high-resolution genetic map of the familial Mediterranean fever candidate region allows identification of haplotype-sharing among ethnic groups. Genomics 44:280-291 . 3. French FMFC. 1997. A candidate gene for familial Mediterranean fever. Nature genetics 17:25-31 .

4. Chae JJ, Wood G, Masters SL, Richard K, Park G, Smith BJ, Kastner DL. 2006. The B30.2 domain of pyrin, the familial Mediterranean fever protein, interacts directly with caspase- 1 to modulate IL-1 beta production. Proceedings of the National Academy of Sciences of the United States of America 103:9982-9987.

5. Ozen S, Bilginer Y. 2014. A clinical guide to autoinflammatory diseases: familial Mediterranean fever and next-of-kin. Nature reviews. Rheumatology 10:135-147.

6. Giancane G, Ter Haar NM, Wulffraat N, Vastert SJ, Barron K, Hentgen V, Kallinich T, Ozdogan H, Anton J, Brogan P, Cantarini L, Frenkel J, Galeotti C, Gattorno M, Grateau G, Hofer M, Kone-Paut I, Kuemmerle-Deschner J, Lachmann HJ, Simon A, Demirkaya E, Feldman B, Uziel Y, Ozen S. 2015. Evidence-based recommendations for genetic diagnosis of familial Mediterranean fever. Annals of the rheumatic diseases 74:635-641 .

7. Berkun Y, Eisenstein EM. 2014. Diagnostic criteria of familial Mediterranean fever. Autoimmunity reviews 13:388-390.

Claims

1 . An in vitro diagnostic method to identify a patient suffering from familial Mediterranean fever (FMF) comprising the following steps:

b. quantifying the level of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 optionally in combination with the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in said sample,

d. identifying a patient suffering from FMF if the level of at least one inflammasome dependent cytokine is at least 2-fold enhanced with respect to the value from an individual not suffering from FMF and/or if the level of at least one inflammasome independent cytokine is at least 4-fold reduced with respect to the value from an individual not suffering from FMF.

2. An in vitro diagnostic method according to claim 1 wherein the peripheral blood mononuclear cells are pretreated with a microtubule polymerization inhibitor prior to incubation with a pyrin-activating microbial agent.

3. An in vitro diagnostic method according to claim 2 wherein said pyrin-activating microbial agent is the Clostridium difficile TcdA toxin and wherein at least one inflammasome dependent cytokine is quantified.

4. An in vitro diagnostic method according to claim 2 wherein said pyrin-activating microbial agent is the Clostridium difficile TcdB toxin and wherein at least one inflammasome independent cytokine is quantified.

5. An in vitro diagnostic method according to claims 1 or 2 wherein the pyrin-activating microbial agent comprises the use of Burkholderia cenocepacia, Clostridium difficile, toxins TcdA and TcdB derived from Clostridium difficile, Clostridium botulinum C3 toxin, Vibrio parahaemolyticus VopS toxin, Histophilus somni IbpA toxin and pertussis toxin.

6. An in vitro diagnostic method according to any one of claims 1 to 5 wherein the peripheral blood mononuclear cells are lymphocytes, monocytes, dendritic cells or macrophages.

7. An in vitro diagnostic method according to any one of claims 1 to 6 wherein the control sample value is a previously determined value from healthy individuals and/or from patients suffering from an autoinflammatory disease different from FMF.

8. A kit for diagnosing FMF comprising a pyrin-activating microbial agent and reagents for detecting at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 optionally in combination with a reagent for detecting at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa.

9. A kit for diagnosing FMF according to claim 8 which also includes a microtubule polymerization inhibitor.

10. A kit for diagnosing FMF according to claims 9 or 10 which includes TcdA and reagents for detecting IL-1 beta or lL-18.

1 1 . A kit for diagnosing FMF according to claims 9 or 10 which includes TcdB and reagents for detecting at least one inflammasome independent cytokine such as for example IL- 4, IL-6, IL-12 or TNF-alfa.

12. A prognostic method for identifying an FMF patient responding to therapy comprising the following steps:

a. quantifying the level of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 optionally in combination with the quantification of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa in a PBMC sample derived from said patient,

c. attributing a response to therapy when the levels of at least one inflammasome dependent cytokine such as IL-1 beta or IL-18 are statistically lower than before the therapy and/or when the levels of at least one inflammasome independent cytokine such as for example IL-4, IL-6, IL-12 or TNF-alfa are statistically higher than before the therapy.

13. A prognostic method according to claim 12 wherein the therapy comprises the use of colchicine, interferon-alpha, TNF-inhibitors or IL-1 antagonists.

14. An in vitro diagnostic method to identify a patient suffering from familial Mediterranean fever (FMF) comprising the following steps:

c. wherein the presence of ASC specks identifies a patient suffering from FMF.